No subject found

1

Hi trying to run the nextflow command, I used the bids validator tool and my datase is Bids-valid but I get this ‘No subject found’ error. I even tried to run it on a dataset on which I was able to run nextlow before (the folders are the same and it’s the same line of command I used before on that dataset), and I still get the same message. Any idea what else I should check? I tried the --input, --bids and --root options

ERROR nextflow.extension.DataflowHelper - @unknown
nextflow.exception.ProcessUnrecoverableException: Error ~ No subjects found. Please check the naming convention, your --input path or your BIDS folder.

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2

Hello,

What are you trying to run? Can you point us to any online documentation?

Best,
Steven

Edit: I see from the tag that you are trying to run TractoFlow. What command are you using?

3

This:
nextflow run tractoflow/main.nf --bids data/ --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity /home/myenv/tractoflow/tractoflow_2.2.1_b9a527_2021-04-13.sif -resume

4

What are the contents of data/?

5

image

6

That looks like the folder name is data3, not data. Also, it might help to enter the full path to data3 In your tractorflow command.

Best,
Steven

7

Yes I did write data3/ in my script, I modify my line depending on which folder I work with and I also tried the full path. It finds the data or data3 folder but it says there are no subjects in it

8

Bumping this issue – I am having the same problem. Running on the same folder where I originally was not getting this error but the directory structure is the same. I am just testing Tractoflow on one subject and, an hour ago, it was able to find the subjects.

Dir structure is: input/e001001/{t1.nii.gz,dwi.nii.gz,bvecs,bvals}, running without BIDS on an interactive HPC node.

singularity.conf file in code just binds current dir for use in the singularity image.

/nafs/narr/nooralsh/nextflow -c /nafs/narr/nooralsh/singularity.conf run /nafs/narr/nooralsh/tractoflow/main.nf --input=/nafs/narr/nooralsh/input/ --fodf_shells "5 1500 3000" -with-singularity /nafs/narr/nooralsh/tractoflow_2.2.1.sif -w /nafs/narr/nooralsh/tf_results/ -resume

NOTE: Nextflow is not tested with Java 1.8.0_282 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.5
Launching `/nafs/narr/nooralsh/tractoflow/main.nf` [ecstatic_minsky] DSL1 - revision: 3fb5c2dda4
TractoFlow pipeline
===================

Start time: 2022-09-27T13:05:54.265-07:00

Max DTI shell extracted: 1200
DTI shells extracted: 5 1500 3000
Input: /nafs/narr/nooralsh/input/
Error ~ No subjects found. Please check the naming convention, your --input path or your BIDS folder.

 -- Check script 'tractoflow/main.nf' at line: 309 or see '.nextflow.log' file for more details
Unknown executor name: ignite

 -- Check script 'tractoflow/main.nf' at line: 352 or see '.nextflow.log' file for more details
9

Hi @nooralsh,

The regular input should be t1.nii.gz/dwi.nii.gz/bval/bvec and not bvecS bvalS
Plus, there is no need for the singularity conf file anymore.

If it does not work please try with tractoflow 2.3.0 + https://scil.usherbrooke.ca/containers/scilus_1.3.0.sif

Hope it helps.
Best,
Arnaud

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10

Thanks @abore, I think removing the ‘s’ and .conf file fixed this error but now I have a new one! I’ll post a new issue since it’s not related to this thread.

Noor

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